DNA AS A TOOL FOR MOLECULAR DISCOVERY - Modern Tools for the Synthesis of Complex Bioactive Molecules - page 537

TABLE 16.1 Representative DNA Catalytic Activities in Nucleic Acid Chemistry

Reaction References

RNA cleavage [11-14]

3 0 -5 0 RNA ligation [15,16]

2 0 -5 0 RNA ligation [17,18]

DNA cleavage [19-21]

DNA phosphorylation [22,23]

DNA ligation [24,25]

DNA depurination [26]

this feature had only been exploited to study the prebiotic replication of nucleic
acids [31-33]. It was only in 2001 that Liu and Gartner introduced the use of DTS to
synthesize small molecules in a one-pot parallel fashion [34]. Their approach relied
on the use of a DNA template bearing a reactive functional group that annealed with a
complementary sequence covalently linked to a reagent, therefore increasing the
effective molarity of the two reactive species. The close proximity allowed the
generation of small molecules chemically unrelated to the DNA that were eventually
separated from the oligonucleotide sequence after cleavage of the carefully designed
linkers (Figure 16.3) [35,36]. The chemical reactivity in DTS was thus entirely
controlled by the effective molarity induced by the hybridization of the complemen-
tary sequences, and therefore reactions did not proceed when single nucleobase
mismatches were introduced into the DNA duplex.
So far, numerous reactions have been shown to be DTS compatible [33-38],
including conjugate additions [34], reductive aminations [35], amine acylations [35],
oxazolidine formation [32], nitro-aldol and nitro-Michael condensations [35], Wittig
olefinations [35], 1,3-nitrone cycloadditions [35], Huisgen cycloadditions [37], and
both Heck and alkene-alkyne coupling reactions [35]. The first example of a DTS
involving a nontethered reagent has also been recently reported [39]. It concerned a
cross-aldolization between a DNA-linked aldehyde, a nontethered ketone, and a
catalyst attached to an oligonucleotide complementary to the DNA sequence that is
bound to the aldehyde component (Figure 16.4).
Another interesting aspect of DTS is the possibility to runmultiple reactions in a
single flask with complete control of the outcome. Hence, by combining 12 DNA-
linked reactive groups in a single solution, Liu and coworkers obtained only six
sequence-programmed products out of the 28 possible products expected under
conventional synthesis (Figure 16.5) [40].
Liu and coworkers also demonstrated the potential of DTS in multistep
synthesis and in vitro selection of libraries containing up to 13,000 synthetic
macrocyclic compounds [38,41]. In a particularly elegant experiment, they encoded
a phenyl sulfonamide group known to confer carbonic anhydrase affinity on one of the
starting DNA templates. A library of 65 macrocyclic fumaramides was thus assem-
bled sequence specifically and subjected to two rounds of selection for carbonic
anhydrase affinity. The macrocyclic fumaramides that contained the phenyl sulfon-
amide group emerged uniquely, therefore demonstrating the potential of DTS to
generate high-affinity binding ligands (Figure 16.6).